#!/usr/bin/perl
foreach(@ARGV) {
    open IN, '<', $_
        or die "Cannot open $_";
    open OUT, '>', "$_.new"
        or die "Cannot create $_.new";

    while(<IN>) {
        s/foo/bar/;
        ...
        print OUT $_;
    }

    close IN;
    close OUT;

    rename "$_.new" "$_";
}